CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections.
Laetitia Fabre,Jian Zhang,Ghislaine Guigon,Simon Le Hello,Véronique Guibert,Marie Accou-Demartin,Saïana de Romans,Catherine Lim,Chrystelle Roux,Virginie Passet,Laure Diancourt,Martine Guibourdenche,Sylvie Issenhuth-Jeanjean,Mark Achtman,Sylvain Brisse,Christophe Sola,François-Xavier Weill +16 more
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TLDR
It was found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type, and spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step.Abstract:
Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool.read more
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Comparative genomics of defense systems in archaea and bacteria
TL;DR: The tight association of the genes encoding immunity systems and dormancy- or cell death-inducing defense systems in prokaryotic genomes suggests that these two major types of defense are functionally coupled, providing for effective protection at the population level.
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Evolutionary Genomics of Defense Systems in Archaea and Bacteria.
TL;DR: Recent comparative genomic studies taking advantage of the expanding database of microbial genomes and metagenomes resulted in the discovery of several previously unknown defense systems, including innate immunity centered on Argonaute proteins, bacteriophage exclusion, and new types of CRISPR-Cas systems of adaptive immunity.
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The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria
TL;DR: Recently reported cases of potential involvement of CRISPR-Cas systems in bacterial stress responses in general and bacterial virulence in particular are described.
Journal ArticleDOI
Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG
François P. Douillard,Angela Ribbera,Angela Ribbera,Ravi Kant,Taija E. Pietilä,Hanna M. Järvinen,Marcel Messing,Cinzia Lucia Randazzo,Lars Paulin,Pia Laine,Jarmo Ritari,Cinzia Caggia,Tanja Lähteinen,Stan J. J. Brouns,Reetta Satokari,Reetta Satokari,Ingemar von Ossowski,Justus Reunanen,Airi Palva,Willem M. de Vos,Willem M. de Vos +20 more
TL;DR: The present study showed two distinctive geno-phenotypes in the L. rhamnosus species, which suggest an adaptation to stable nutrient-rich niches and adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.
Journal ArticleDOI
Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa
Alex van Belkum,Leah Soriaga,Matthew C. LaFave,Srividya Akella,Jean-Baptiste Veyrieras,E. Magda Barbu,Dee Shortridge,Bernadette Blanc,Gregory Hannum,Gilles Zambardi,Kristofer Miller,Mark C. Enright,Nathalie Mugnier,Daniel Brami,Stéphane Schicklin,Martina Felderman,Ariel S. Schwartz,Toby Richardson,Todd C. Peterson,Bolyn Hubby,Kyle C. Cady +20 more
TL;DR: It is demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields.
References
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Journal ArticleDOI
CRISPR provides acquired resistance against viruses in prokaryotes
Rodolphe Barrangou,Christophe Fremaux,Hélène Deveau,Melissa Richards,Patrick Boyaval,Sylvain Moineau,Dennis A. Romero,Philippe Horvath +7 more
TL;DR: It is found that, after viral challenge, bacteria integrated new spacers derived from phage genomic sequences, and CRISPR provided resistance against phages, and resistance specificity is determined by spacer-phage sequence similarity.
Journal ArticleDOI
Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity.
Paul R. Hunter,M A Gaston +1 more
TL;DR: An index of discrimination for typing methods is described, based on the probability of two unrelated strains being characterized as the same type, which may be used to compare typing methods and select the most discriminatory system.
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Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology.
Judith Kamerbeek,Leo M. Schouls,Arend H. J. Kolk,M van Agterveld,D. van Soolingen,Sjoukje Kuijper,Annelies Bunschoten,H Molhuizen,R J Shaw,M Goyal,J. D. A. Van Embden +10 more
TL;DR: A novel method based on strain-dependent hybridization patterns of in vitro-amplified DNA with multiple spacer oligonucleotides was found to differentiate M. bovis from M. tuberculosis, a distinction which is often difficult to make by traditional methods.
Journal ArticleDOI
CRISPR/Cas, the Immune System of Bacteria and Archaea
TL;DR: Clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide acquired immunity against viruses and plasmids by targeting nucleic acid in a sequence-specific manner.
Journal ArticleDOI
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA.
Josiane E. Garneau,Marie Ève Dupuis,Manuela Villion,Dennis A. Romero,Rodolphe Barrangou,Patrick Boyaval,Christophe Fremaux,Philippe Horvath,Alfonso H. Magadán,Sylvain Moineau +9 more
TL;DR: In vivo evidence is provided that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading toplasmid loss.